BN0452 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 9.8329e-09 1.9384e-05
Layer 3 7.9675e-08 1.1599e-03
Layer 2 1.6489e-06 1.0944e-03
Layer 5 2.3154e-05 2.0667e-04
Layer 6 5.1018e-05 4.0817e-03
Layer 1 9.7405e-01 6.8208e-01
WM 9.9608e-01 7.3458e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SIRPA Expression Distribution
Gene Specificity Score (GSS)
SIRPA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SIRPA Layer 4 2.7363 0.7834
CAMK1D Layer 4 2.6602 0.7821
SV2A Layer 5 2.7852 0.7776
CTBP1 Layer 4 2.5664 0.7750
GABBR2 Layer 4 2.5781 0.7747
COPRS Layer 4 2.3281 0.7744
TOLLIP Layer 4 2.4727 0.7731
PRPF19 Layer 4 2.5059 0.7725
KCNA2 Layer 4 2.5957 0.7695
CNTNAP2 Layer 4 3.4688 0.7694
CPLX1 Layer 4 2.6250 0.7693
DNAJC6 Layer 4 2.6250 0.7685
RAB6A Layer 4 2.5840 0.7679
TUBB4B Layer 4 2.5840 0.7671
TCEA2 Layer 4 2.4121 0.7671
NDUFS2 Layer 5 2.4775 0.7670
PSMC5 Layer 4 2.5957 0.7666
BMERB1 Layer 4 2.6660 0.7656
RBFOX2 Layer 4 2.7363 0.7650
UBA1 Layer 4 2.4512 0.7644
CALY Layer 5 2.5957 0.7638
ABAT Layer 4 2.7246 0.7634
ATXN7L3B Layer 4 2.8398 0.7632
GNG3 Layer 5 2.6191 0.7632
PRDX2 Layer 4 2.3867 0.7629
INPP5F Layer 4 2.4727 0.7621
MAPK10 Layer 4 2.7188 0.7620
SULT4A1 Layer 4 2.8906 0.7619
FYN Layer 5 2.3125 0.7615
SCAMP5 Layer 4 2.6777 0.7614
ATP6AP2 Layer 5 2.3965 0.7610
MAPK8IP1 Layer 5 2.3184 0.7605
TUBB3 Layer 5 2.6982 0.7598
CIRBP Layer 4 2.7070 0.7596
CA11 Layer 4 2.7246 0.7592
TBCB Layer 5 2.4482 0.7592
DYNLL2 Layer 4 2.5664 0.7590
CTNNB1 Layer 4 2.6426 0.7588
SLC12A5 Layer 4 2.7129 0.7587
GABRG2 Layer 4 2.5566 0.7586
HSPH1 Layer 5 2.3574 0.7585
PAFAH1B2 Layer 4 2.7246 0.7584
GABRA1 Layer 4 2.5215 0.7582
GRK2 Layer 4 2.4941 0.7576
CCDC92 Layer 5 2.4971 0.7576
ATP5F1D Layer 4 2.6191 0.7575
ATP1A1 Layer 4 2.5332 0.7572
ATCAY Layer 4 2.5664 0.7571
SERPINI1 Layer 4 2.5664 0.7570
MAGED1 Layer 5 2.5898 0.7569

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0452
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0452_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0452/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0452/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0452/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0452/report/PD/BN0452_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0452/report/PD/BN0452_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:10:46
  • Number of Processes: 10
  • Spending Time: 0h 2m